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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattttagcccaaatatctattcatgtatgatatattctgagattaatattctaacatggctttaaaaatgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTG

Basic information

species Oryza sativa
transcript LOC_Os01g51220.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G439457_T01 (Zea mays), 3'ss of exon 6
gtgaggattttagcccaaatatctattcatgtatgatatattctgagattaatattctaacatggctttaaaaatgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTG
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gtagaaattccagtactagtgacagatgacct-tatcattttgttgaagcaatatgtcaacattactttgtaactttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTGCCAATTGAAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88661963|gb|CI460991.1|CI460991
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|87031904|gb|CI268133.1|CI268133
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88488420|gb|CI425691.1|CI425691
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88484151|gb|CI421422.1|CI421422
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88243947|gb|CI243069.1|CI243069
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88516373|gb|CI444027.1|CI444027
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88520758|gb|CI446414.1|CI446414
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88281784|gb|CI403180.1|CI403180
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|12622960|gb|AU173173.1|AU173173
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88281957|gb|CI403353.1|CI403353
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88489179|gb|CI426451.1|CI426451
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
EST: gi|88519872|gb|CI447526.1|CI447526
EST:     AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGG                         GGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG
genomic: AGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 67 (downstream exon)
Score: 26

GTTCATTTCGGTGCCCAAGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattt ... atgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatgatatattctgagattaatattctaacatggctttaaaaatgtttgtagGGTGTACTGGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTG
                          ttctaac  putative branch site (score: 26)
       atatattctgagatta  TA-rich tract